rs6906871

Positions:

• chr6-136641079-C-A
• chr6-136641079-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005923.4(MAP3K5):​c.1838+1441G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,016 control chromosomes in the GnomAD database, including 24,570 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24570 hom., cov: 33)
• Consequence: MAP3K5 NM_005923.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

Genes affected

MAP3K5 (HGNC:6857): (mitogen-activated protein kinase kinase kinase 5) Mitogen-activated protein kinase (MAPK) signaling cascades include MAPK or extracellular signal-regulated kinase (ERK), MAPK kinase (MKK or MEK), and MAPK kinase kinase (MAPKKK or MEKK). MAPKK kinase/MEKK phosphorylates and activates its downstream protein kinase, MAPK kinase/MEK, which in turn activates MAPK. The kinases of these signaling cascades are highly conserved, and homologs exist in yeast, Drosophila, and mammalian cells. MAPKKK5 contains 1,374 amino acids with all 11 kinase subdomains. Northern blot analysis shows that MAPKKK5 transcript is abundantly expressed in human heart and pancreas. The MAPKKK5 protein phosphorylates and activates MKK4 (aliases SERK1, MAPKK4) in vitro, and activates c-Jun N-terminal kinase (JNK)/stress-activated protein kinase (SAPK) during transient expression in COS and 293 cells; MAPKKK5 does not activate MAPK/ERK. [provided by RefSeq, Jul 2008]

MAP3K5-AS1 (HGNC:40358): (MAP3K5 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP3K5	NM_005923.4	c.1838+1441G>T		intron_variant		ENST00000359015.5	NP_005914.1
MAP3K5-AS1	NR_125858.1	n.335+3977C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP3K5	ENST00000359015.5	c.1838+1441G>T		intron_variant		1	NM_005923.4	ENSP00000351908	P1
MAP3K5-AS1	ENST00000432477.2	n.383+3977C>A		intron_variant, non_coding_transcript_variant		2
MAP3K5	ENST00000698928.1	c.2165+1441G>T		intron_variant				ENSP00000514039

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84834 AN: 151898 Hom.: 24572 Cov.: 33

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.584

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.558 AC: 84848 AN: 152016 Hom.: 24570 Cov.: 33 AF XY: 0.556 AC XY: 41293 AN XY: 74286

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.576

Alfa AF: 0.583 Hom.: 3255

Bravo AF: 0.549

Asia WGS AF: 0.607 AC: 2109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	11
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6906871; hg19: chr6-136962217; COSMIC: COSV62891741;